Pathogens and certain diseases can be identified in the environment or in a patient by detecting DNA associated with the pathogen or disease in environmental samples, body fluids, water, or other contaminated solutions. DNA can also be extracted from crime scenes and associated evidence. It is generally necessary to concentrate DNA before the DNA can be identified. DNA can be concentrated by filtration. However, filtration technologies are inefficient. Filters fine enough to trap DNA, viruses or the like are easily clogged with other debris. There is a general need for technologies capable of concentrating DNA and similar materials and/or extracting relatively pure DNA from contaminated solutions.
Laborious and/or expensive purification methods are often employed to prepare samples containing nucleic acids for biochemical assays. The polymerase chain reaction (PCR) can be used to amplify the concentrations of nucleic acids such as DNA and RNA. However, PCR can be undesirably expensive, especially for large volume samples.
Electrophoresis involves directing the movement of charged particles in a medium, such as a gel or liquid solution by applying an electric field across the medium. The electric field may be generated by applying a potential across electrodes that are placed in contact with the medium such that electric current can be conducted into the medium. The movement of the particles in the medium is affected by the magnitude and direction of the electric field, the electrophoretic mobility of the particles and the mechanical properties, such as viscosity, of the medium. Through electrophoresis, particles that are distributed in a medium can be transported through the medium. Electrophoresis is commonly used to transport nucleic acids (such as DNA or RNA) through gel substrates. Since different species have different electrophoretic mobilities, electrophoresis may be used to separate different species from one another. Conventional electrophoresis techniques are largely limited in application to the linear separation of charged particles. Using conventional electrophoresis techniques, a direct current (DC) electric field or an alternating pulsed-field electrophoretic (PFGE) field is typically applied to a medium so that particles in the medium are transported toward an electrode.
Electrophoresis may be used to transport fragments of DNA or other microscopic electrically charged particles. Various electrophoresis methods are described in Slater, G. W. et al. Electophoresis 2000, 21, 3873-3887. Electrophoretic particle transport is typically performed in one dimension by applying a direct current (DC) electric field between electrodes on either side of a suitable electrophoresis gel. The electric field causes electrically charged particles in the gel to move toward one of the electrodes. Electrophoresis is typically used to separate particles of different types from one another.
Electrophoresis can also be used to concentrate particles in a particular location. A problem that can interfere with the successful use of electrophoresis for concentrating particles in some applications is that there must be an electrode at the location where the particles are to be concentrated. Electrochemical interactions between the electrodes and particles can degrade certain kinds of the particles. For example, where the particles comprise DNA, the DNA can be damaged by electrochemical interactions at the electrodes.
Electric fields present during conventional direct current electrophoresis are divergence-free everywhere except at electrodes which can source or sink electric current. Electrophoresis is typically applied in cases where particles are caused to move toward an electrode.
An asymmetric alternating current (AC) waveform can cause net drift of electrophoretic particles due to nonlinearity of the relationship between particle speed and applied electric field. This effect can be used to cause particles to move in one dimension as described in Chacron, M. J., et al. Phys. Rev. E 1997, 56, 3446-3450; Frumin, L. L, et al. Phys. Chem. Commun. 2000, 11; and, Frumin, L. L. et al. Phys. Rev. E 2001, 64, 021902.
Pohl, H. A., Dielectrophoresis: The Behavior of Neutral Matter in Nonuniform Electric Fields Cambridge University Press, Cambridge, UK 19.78; Asbury, C. L., et al., Electrophoresis 2002, 23, 2658-2666; and Asbury, C. L., et al. Biophys. J. 1998, 74, 1024-1030 disclose that dielectrophoresis can be applied to concentrate DNA in two or more dimensions. However, practical applications of dielectrophoresis require undesirably high electric field gradients.
One can isolate particles which have been separated from other particles by electrophoresis by cutting out the portion of the medium in which the particles have been carried by electrophoresis. The particles can be separated from the medium by using various purification techniques.
References which describe methods for DNA separation include: Slater et al. The theory of DNA separation by capillary electrophoresis Current Opinion in biotechnology 2003 14:58-64; Slater et al. U.S. Pat. No. 6,146,511 issued 14 Nov. 2000; Frunin et al. Nonlinear focusing of DNA macromolecules Phys. Rev. E 64:021902; Griess et al. Cyclic capillary electrophoresis Electrophoresis 2002, 23, 2610-2617 Wiley-VCH Verlag GmbH & Co. Weinheim (2002). References which describe the use of fields to separate particles include: Bader et al. U.S. Pat. No. 5,938,904 issued on Aug. 17, 1999; Bader et al. U.S. Pat. No. 6,193,866 issued on 27 Feb. 2001; Tessier et al: Strategies for the separation of polyelectrolytes based on non-linear dynamics and entropic ratchets in a simple microfluidic device Appl. Phys. A 75, 285-291 (2002); Chacron et al. Particle trapping and self-focusing in temporally asymmetric ratchets with strong field gradients Phys. Rev. B 56:3 3446-3550 (September 1997); Dean et al. Fluctuation driven ratchets: molecular motors Phys. Rev. Lett. 72:11 1766-1769 (14 Mar. 1994); Bier et al. Biasing Brownian motion in different directions in a 3-state fluctuating potential and an application for the separation of small particles Phys. Rev. Lett. 76:22 4277-4280 (27 May, 1996); Magnasco, forced thermal ratchets Phys. Rev. Lett. 71:10 1477-1481 (6 Sep. 1993).
There remains a need for methods for moving and/or concentrating particles that improve on prior art methods and avoid limitations of prior art methods in specific applications. There also remains a need for effective methods for extracting materials such as DNA from media such as gels.